Search Results (101)

Single-nucleotide polymorphism (SNP) genotyping arrays are important tools for crop genetic research. Addressing the current issues of insufficient accuracy in upland cotton cultivar identification and difficulties in distinguishing closely related germplasm and hybrids, developing an SNP array enabling rapid and accurate cotton cultivar identification and applicable to molecular breeding is a key demand in cotton cultivar identification and genetic breeding. This study aims to develop a low-cost and high-precision SNP array for upland cotton (Gossypium hirsutum L.) based on Genotyping by Target Sequencing (GBTS) technology. The array will integrate high accuracy in cultivar identification with applicability to molecular breeding, and this study further aims to clarify its application in cultivar identification. The Cotton 13K SNP array contains 13,571 high-quality SNP loci, including 8658 polymorphic sites derived from resequencing data and 4913 functional loci linked to key agronomic traits. All these loci are relatively evenly distributed across the genome. Genotyping 219 upland cotton cultivars/lines accurately clustered them into four genetic subgroups (K = 4), which closely matched their breeding institutions and geographical origins. Analysis of 44 experimental cotton materials (including sister lines and backcross materials) established a genetic similarity threshold of ≥90% for effectively distinguishing closely related germplasm. Comparative analysis of 38 F₁ hybrids and conventional cotton cultivars demonstrated that the average heterozygosity (Het) of hybrids (16.01%) was significantly higher than that of conventional cultivars (5.52%, p < 0.001). A preliminary threshold of Het ≥ 10% was identified for accurate discrimination of cotton hybrids. In conclusion, the Cotton 13K SNP array is a robust tool for population genetic analysis, discrimination of closely related cultivars, and hybrid identification. It also facilitates key molecular breeding steps, including parental evaluation, backcross monitoring, and marker-assisted selection (MAS). Its integration into breeding pipelines is expected to accelerate the development of new cotton varieties. Full article

Background: Sucrose metabolism plays a crucial role in plant responses to abiotic stresses such as drought and high temperatures, significantly influencing plant growth and yield formation. In higher plants, the second step in sucrose bioconversion involves sucrose phosphate phosphatase (SPP) hydrolyzing sucrose-6-phosphate to form sucrose. This study determined the number of SPP gene family members in upland cotton (Gossypium hirsutum), systematically analyzed their fundamental characteristics, physicochemical properties, phylogenetic relationships, chromosomal localization, and expression patterns across different tissues and under various abiotic stresses. Methods: The SPP gene family in hirsutum was identified using Hidden Markov Models (HMMER) and the NCBI Conserved Domain Database (NCBI CDD), and its physico-chemical properties were analyzed via the SOPMA online analysis website. Phylogenetic relationships were determined using MEGA 12.0 software. Promoter regions were analyzed with PlantCARE, sequence patterns were identified via MEME, and transcriptome data were downloaded from the CottonMD database. Results: This study identified four members of the hirsutum SPP gene family, with amino acid lengths ranging from 335 to 1015, molecular weights between 38.38 and 113.28 kDa, and theoretical isoelectric points (pI) between 5.39 and 6.33. These genes are localized across four chromosomes. The SPP gene family in hirsutum exhibits closer phylo-genetic relationships with SPP genes in Arabidopsis thaliana and Chenopodium quinoa. Their promoter regions are rich in cis-elements associated with multiple abiotic stress resistance functions, and their expression patterns vary across different tissues and under different abiotic stress conditions. Conclusions: The GhSPP gene may play an important role in the growth and development of upland cotton and its responses to salt stress and drought. Therefore, it could be considered as a candidate gene for future functional analysis of cotton resistance to salt and drought stress. Full article

Upland cotton (Gossypium hirsutum L.) is a major global commodity crop whose production is threatened by the reniform nematode (Rotylenchulus reniformis Linford and Oliveira), a plant-parasitic pest that causes substantial yield losses. Host-plant resistance offers a sustainable management strategy, but currently available resistant cotton cultivars provide only partial protection and often require supplemental control methods. In this study, Clustered Regularly Interspaced Palindromic Repeats (CRISPR)–CRISPR-associated 9 (Cas9) gene editing was used to generate targeted knockouts of Mildew Resistance Locus O (GhiMLO3) in cotton and assess its role in resistance to R. reniformis. Four independent knockout lines (A1, D3, E1, and P3) were developed, confirmed by sequencing, and evaluated for nematode resistance under controlled greenhouse conditions. Nematode reproduction was significantly reduced on lines D3 and E1, with lower egg counts and fewer vermiform life stages compared with the control genotypes, Coker 312 (WT), Delta Pearl, and Jin668. The edited lines also showed characteristic mesophyll cell-death phenotypes, suggesting potential pleiotropic effects associated with MLO-mediated resistance. Sequence analysis confirmed multiple homozygous and heterozygous mutations in MLO3 alleles from both the A and D subgenomes, with D3 and E1 lines displaying the strongest resistance profiles. These findings demonstrate that MLO3 gene editing is a promising approach for improving R. reniformis resistance in cotton. Full article

Cotton is a vital economic crop, and cotton fiber serves as the primary raw material for the textile industry. Lignin in cotton fiber is closely associated with fiber quality. Lignin is synthesized through the phenylpropanoid metabolic pathway, where the cinnamyl alcohol dehydrogenase gene CAD6 plays a significant role. In this study, we obtained successfully transformed overexpression plants by constructing an overexpression vector and performing genetic transformation and tissue culture. To verify the function of the GhCAD6 gene in upland cotton, we analyzed the agronomic traits, fiber quality, cell wall structure, and lignin content of GhCAD6-overexpressing plants. Our results indicate that the GhCAD6 gene is predominantly expressed during the stages of fiber elongation and secondary wall synthesis. Overexpression of the GhCAD6 gene resulted in increased plant lignin content and fiber upper half mean length, boll number per plant, fiber uniformity index, strength, and lint were improved. The fiber surface was smoother, and the fiber cell wall was more compact. These findings demonstrate that the GhCAD6 gene positively regulates lignin synthesis and fiber quality formation, contributing to the enhancement of cotton fiber quality. Full article

Cotton fiber quality improvement remains a fundamental challenge in breeding programs due to the complex genetic architecture underlying fiber development. The narrow genetic base of upland cotton (Gossypium hirsutum L.) and the quantitative nature of fiber quality traits necessitate innovative approaches for identifying and incorporating superior alleles from related species. We developed a BC₆F₂ population by introgressing chromosome segments from the sea island cotton variety Xinhai 36 (G. barbadense) into the upland cotton variety Xinluzhong 60 (G. hirsutum). Based on fiber strength phenotyping, we constructed two DNA bulks representing extreme phenotypes (20 superior and 12 inferior individuals) for bulked segregant analysis sequencing (BSA-Seq). High-throughput sequencing generated 225.13 Gb of raw data with average depths of 20× for parents and 30× for bulks. SNP calling and annotation were performed using GATK and ANNOVAR against the upland cotton reference genome (TM-1). BSA-Seq analysis identified 13 QTLs primarily clustered within a 1.6 Mb region (20.6–22.2 Mb) on chromosome A10. Within this region, we detected nonsynonymous mutation genes involving a total of six genes. GO and KEGG enrichment analyses revealed significant enrichment for carbohydrate metabolic processes, protein modification, and secondary metabolite biosynthesis pathways. Integration with transcriptome data prioritized GH_A10G1043, encoding a β-amylase family protein, as the key candidate gene. Functional validation through overexpression and RNAi knockdown in Arabidopsis thaliana demonstrated that GH_A10G1043 significantly regulates starch content and β-amylase activity, though without visible morphological alterations. This study successfully identified potential genomic regions and candidate genes associated with cotton fiber strength using chromosome segment substitution lines combined with BSA-Seq. The key candidate gene GH_A10G1043 provides a valuable target for marker-assisted selection in cotton breeding programs. Our findings establish a foundation for understanding the molecular mechanisms of fiber quality formation and offer genetic resources for developing superior cotton varieties with enhanced fiber strength. Full article

Cottonseeds, rich in high-quality protein and fatty acids, represent a vital plant-derived feedstuff and edible oil resource. To systematically investigate genetic variation patterns in nutritional quality and screen superior germplasm, this study analyzed 26 nutritional quality traits and 8 fiber traits across 259 upland cotton (Gossypium hirsutum L.) accessions using multivariate statistical approaches. Results revealed significant genetic diversity in cottonseed nutritional profiles, with coefficients of variation ranging from 3.42% to 26.37%. Moreover, with advancements in breeding periods, the contents of protein, amino acids, and the proportion of unsaturated fatty acids (UFAs) increased, while oil content and C16:0 levels decreased. Correlation analyses identified significant positive associations (p < 0.05) between proteins, amino acids, UFAs, and most fiber traits, except for seed index (SI), fiber micronaire (FM), and fiber elongation (FE). Through a principal component analysis–fuzzy membership function (PCA-FMF) model, 13 elite accessions (F > 0.75) with high protein content, high UFA proportion, and excellent fiber quality were identified. These findings provide both data-driven foundations and practical germplasm resources for value-added utilization of cottonseed and coordinated breeding for dual-quality traits of nutrition and fiber. Full article

Background: Gossypium hirsutum L. is one of the main economic crops worldwide, and increasing the size/weight of its seeds is a potential strategy to improve its seed-related yield. AINTEGUMENTA (ANT) is an organogenesis transcription factor mediating cell proliferation and expansion in Arabidopsis, but little is known about its candidate function in upland cotton seed. Results: In this study, functional characterization of GhANT in the cotton seed development stage was performed. The expression pattern analysis showed that GhANT was predominantly expressed in the ovules, and its expression was consistent with the ovules’ development stage. Heterologous expression of GhANT in Arabidopsis promoted plant organ growth and led to larger seeds. Importantly, specific expression of GhANT by the TFM7 promoter in the cotton ovules enlarged the seeds and increased the cotton seed yield, as compared with the wild-type in a three-year field trial. Furthermore, transcription level analysis showed that numerous genes involved in cell division were up-regulated in the ovules of TFM7::GhANT lines in comparison to the wild-type. These results indicate that GhANT is a potential genetic resource for improving cotton seed yield through its molecular links with cell cycle controllers. Full article

Background: The B3-domain transcription factor ABI3 (ABSCISIC ACID INSENSITIVE 3) is a critical regulator of seed maturation, stress adaptation, and hormonal signaling in plants. However, its evolutionary dynamics and functional roles in cotton (Gossypium spp.) remain poorly characterized. Methods: We conducted a comprehensive genome-wide investigation of the ABI3 gene family across 26 plant species, with a focus on 8 Gossypium species. Analyses included phylogenetics, chromosomal localization, synteny assessment, gene duplication patterns, protein domain characterization, promoter cis-regulatory element identification, and tissue-specific/spatiotemporal expression profiling under different organizations of Gossypium hirsutum. Results: Phylogenetic and chromosomal analyses revealed conserved ABI3 evolutionary patterns between monocots and dicots, alongside lineage-specific expansion events within Gossypium spp. Syntenic relationships and duplication analysis in G. hirsutum (upland cotton) indicated retention of ancestral synteny blocks and functional diversification driven predominantly by segmental duplication. Structural characterization confirmed the presence of conserved B3 domains in all G. hirsutum ABI3 homologs. Promoter analysis identified key stress-responsive cis-elements, including ABA-responsive (ABRE), drought-responsive (MYB), and low-temperature-responsive (LTRE) motifs, suggesting a role in abiotic stress regulation. Expression profiling demonstrated significant tissue-specific transcriptional activity across roots, stems, leaves, and fiber developmental stages. Conclusions: This study addresses a significant knowledge gap by elucidating the evolution, structure, and stress-responsive expression profiles of the ABI3 gene family in cotton. It establishes a foundational framework for future functional validation and targeted genetic engineering strategies aimed at developing stress-resilient cotton cultivars with enhanced fiber quality. Full article

Advances in spinning technology have increased the demand for upland cotton (Gossypium hirsutum L.) cultivars with superior fiber quality. However, progress in breeding for traits such as fiber length is constrained by limited phenotypic and genetic diversity within upland cotton. Introgression from Gossypium barbadense, a closely related species known for its superior fiber traits, offers a promising strategy. Sealand 883 is an obsolete upland germplasm developed through G. barbadense introgression and is known for its long and fine fibers. Previous studies have identified a fiber length quantitative trait locus (QTL) on Chromosome 25, designated qFL-Chr.25, in Sealand 883, conferred by an allele introgressed from G. barbadense. This study evaluated the effect of qFL-Chr.25 in near-isogenic introgression lines (NIILs) using Advanced Fiber Information System (AFIS) measurements. Across four genetic backgrounds, NIILs carrying qFL-Chr.25 consistently exhibited longer fibers, as reflected in multiple length parameters, including UHML, L(n), L(w), UQL(w), and L5%. Newly developed TaqMan SNP diagnostic markers flanking the QTL enable automated, reproducible, and scalable screening of large populations typical in commercial breeding programs. These markers will facilitate the incorporation of qFL-Chr.25 into commercial breeding pipelines, accelerating fiber quality improvement and enhancing the competitiveness of cotton against synthetic fibers. Full article

Phosphorus (P) is an essential nutrient for plant growth, and low-phosphorus (LP) stress significantly limits cotton productivity. Here, we conducted single- and multi-locus genome-wide association studies (GWASs) on four LP-related traits using 419 upland cotton (Gossypium hirsutum L.) accessions genotyped with 2.97 million single-nucleotide polymorphisms (SNPs). Phenotypic analysis reveals substantial variation under LP stress, with LP-SDW showing the highest coefficient of variation (33.69%). The GWASs identified thousands of significant SNPs, including pleiotropic loci associated with multiple traits. Chromosomes A08, D09, and D12 harbored novel associated signals. Multi-locus models significantly enhanced detection sensitivity, identifying 123 SNPs undetected by single-locus approaches. Functional annotations prioritized six candidate genes near associated SNPs, including GhM_A08G1315 (remorin protein) and GhM_D06G1152 (carotenoid cleavage dioxygenase), whose LP-induced expression patterns were validated by qRT-PCR. These genes are implicated in membrane signaling, root architecture modulation, and hormone metabolism. Our findings provide novel genetic insights into LP tolerance and establish a foundation for breeding phosphorus-efficient varieties through marker-assisted selection in cotton. Full article

Cotton leaf curl Kokhran virus-Burewala (CLCuKoV-Bur) has a circular single-stranded ssDNA genome of 2759 nucleotides in length and belongs to the genus Begomovirus (family, Geminiviridae). CLCuKoV-Bur causes cotton leaf curl disease (CLCuD) and is transmitted by the whitefly Bemisis tabaci cryptic species. Monopartite begomoviruses encode five open reading frames (ORFs). CLCuKoV-Bur replicates through a dsDNA intermediate. Five open reading frames (ORFs) are organized in the small circular, single-stranded (ss)-DNA genome of CLCuKoV-Bur (2759 bases). RNA interference (RNAi) is a naturally occurring process that has revolutionized the targeting of gene regulation in eukaryotic organisms to combat virus infection. The aim of this study was to elucidate the potential binding attractions of cotton-genome-encoded microRNAs (Gossypium hirsutum-microRNAs, ghr-miRNAs) on CLCuKoV-Bur ssDNA-encoded mRNAs using online bioinformatics target prediction tools, RNA22, psRNATarget, RNAhybrid, and TAPIR. Using this suite of robust algorithms, the predicted repertoire of the cotton microRNA-binding landscape was determined for a CLCuKoV-Bur consensus genome sequence. Previously experimentally validated cotton (Gossypium hirsutum L.) miRNAs (n = 80) were selected from a public repository miRNA registry miRBase (v22) and hybridized in silico into the CLCuKoV-Bur genome (AM421522) coding and non-coding sequences. Of the 80 ghr-miRNAs interrogated, 18 ghr-miRNAs were identified by two to four algorithms evaluated. Among them, the ghr-miR399d (accession no. MIMAT0014350), located at coordinate 1747 in the CLCuKoV-Bur genome, was predicted by a consensus or “union” of all four algorithms and represents an optimal target for designing an artificial microRNA (amiRNA) silencing construct for in planta expression. Based on all robust predictions, an in silico ghr-miRNA-regulatory network was developed for CLCuKoV-Bur ORFs using Circos software version 0.6. These results represent the first predictions of ghr-miRNAs with the therapeutic potential for developing CLCuD resistance in upland cotton plants. Full article

Background/Objectives: The classification and phylogenetic relationships of Gossypium hirsutum L. landraces, despite their proximity to southern Mexico, remain unresolved. This study aimed to clarify these relationships using SSR markers and hybridization methods, focusing on subspecies and race differentiation within G. hirsutum L. Methods: Seventy polymorphic SSR markers (out of 177 tested) were used to analyze 141 alleles and calculate genetic distances among accessions. Phylogenetic relationships were determined using MEGA software (version 11.0.13) and visualized in a phylogenetic tree. ANOVA in NCSS 12 was used for statistical analysis. Over 1000 inter-race crosses were conducted to assess boll-setting rates. Results: Distinct phylogenetic patterns were identified between G. hirsutum subspecies and races, correlating with boll-setting rates. Latifolium, richmondii, and morilli showed no significant increase in boll-setting rates in reciprocal crosses. Cultivars Omad and Bakht, as paternal parents, yielded higher boll-setting rates. Religiosum and yucatanense displayed high boll- and seed-setting rates as maternal parents but low rates as paternal parents. Additionally, phylogenetic analysis revealed a close relationship between cultivars ‘Omad’ and ‘Bakht’ with G. hirsutum race richmondii, indicating their close evolutionary relationship. Conclusions: Reciprocal differentiation characteristics of G. hirsutum subspecies and races, particularly religiosum and yucatanense, should be considered during hybridization for genetic and breeding studies. Understanding the phylogenetic relationships among G. hirsutum taxa is crucial for exploring the genetic diversity of this economically important species. Full article

The trithorax group (TrxG) complex is an important protein in the regulation of plant histone methylation. The ABSENT, SMALL, OR HOMEOTIC DISCS 1 (ASH1) gene family, as important family members of the TrxG complex, has been shown to regulate tolerance to abiotic stress and growth and development in many plants. In this study, we identified nine GhASH1s in upland cotton. Bioinformatics analysis revealed that GhASH1s contain a variety of cis-acting elements related to stress resistance and growth and development. The transcriptome expression profiles revealed that GhASHH1.A and GhASHH2.A genes expression were upregulated in flower organs and in response to external temperature stress. The results of virus-induced gene silencing (VIGS) indicated that GhASHH1.A and GhASHH2.A genes silencing reduced the ability of cotton to adapt to temperature stress and delayed the development of the flowering phenotype. We also showed that the silencing of these two target genes did not induce early flowering at high temperature (32 °C), suggesting that GhASHH1.A and GhASHH2.A might regulate cotton flowering in response to temperature. These findings provide genetic resources for future breeding of early-maturing and temperature-stress-tolerant cotton varieties. Full article

Cotton is one of the world’s leading fiber crops, but climate change, drought, heat, and salinity have significantly decreased its production, consequently affecting the textile industries globally. To acclimate to these environmental challenges, a number of gene families involved in various molecular, physiological, and hormonal mechanisms play crucial roles in improving plants response to various abiotic stresses. One such gene family is the GhSRF, a Strubbelig-Receptor family (SRF), and member of the leucine-rich repeat (LRR-V) group. This family encodes leucine-rich repeat transmembrane receptor-like kinases (LRR-RLKs) and have not yet been explored in cotton. Arabidopsis thaliana Strubbelig-Receptor gene sequences were used as queries to identify the homologs in cotton, with subsequent support from the literature and functional prediction through online data. In the current study, a comprehensive genome-wide analysis of cotton was conducted, identifying 22 SRF putative proteins encoded by 22 genes. We performed the detailed analysis of these proteins, including phylogeny, motif and gene structure characterization, promoter analysis, gene mapping on chromosomes, gene duplication events, and chromosomal sub-cellular localization. Expression analysis of putative genes was performed under drought and heat stress conditions using publicly available RNAseq data. The qRT-PCR results showed elevated expression of GhSRF2, GhSRF3, GhSRF4, GhSRF10, and GhSRF22 under drought and heat stress. So, it could be speculated that these genes may play a role in drought and heat tolerance in cotton. These findings could be helpful in cotton breeding programs for the development of climate-resilient cultivars. Full article

Genome-wide association study (GWAS) has identified numerous significant loci for boll number (BN) and boll weight (BW), which play an essential role in cotton (Gossypium spp.) yield. The North Carolina design II (NC II) genetic mating population exhibits a greater number of genetic variations than other populations, which may facilitate the identification of additional genes. Accordingly, the 3VmrMLM method was employed for the analysis of upland cotton (Gossypium hirsutum L.) in an incomplete NC II genetic mating population across three environments. A total of 204 quantitative trait nucleotides (QTNs) were identified, of which 25 (24.75%) BN and 30 (29.13%) BW QTNs were of small effect (<1%) and 24 (23.76%) BN and 20 (19.42%) BW QTNs were rare (<10%). In the vicinity of these QTNs, two BN-related genes and two BW-related genes reported in previous studies were identified, in addition to five BN candidate genes and six BW candidate genes, which were obtained using differential expression analysis, gene function annotation, and haplotype analysis. Among these, six candidate genes were identified as homologs of Arabidopsis genes. The present study addresses the limitation of heritability missing and uncovers several new candidate genes. The findings of this study can provide a basis for further research and marker-assisted selection in upland cotton. Full article